1.Development and validation of PhenoRAG: A visualization tool for automated human phenotype ontology term annotation based on large language models and retrieval-augmented generation technology.
Wei ZHONG ; Yousheng YAN ; Kai YANG ; Yan LIU ; Xinyu FU ; Zhengyang YAO ; Chenghong YIN
Chinese Journal of Medical Genetics 2026;43(1):36-43
OBJECTIVE:
To develop a user-friendly visualization application for the automatic annotation of Human Phenotype Ontology (HPO) terms based on large language models and retrieval-augmented generation (RAG) technology, and to validate its performance in an authoritative case dataset.
METHODS:
By integrating the domestic open-source large language model DeepSeek-V3 with RAG technology, an interactive web application was deployed on the Streamlit cloud platform. Using only the latest official HPO dataset as the data source, the lightweight sentence-embedding model BAAI/bge-small-en-v1.5 was employed to construct a FAISS vector index. During the online phase, a four-step closed-loop process is automatically completed: multilingual translation, phenotype phrase extraction, RAG candidate retrieval, term mapping, and official database validation. 121 English case reports publicly released by BMJ Case Reports and Oxford Medical Case Reports (with a gold-standard HPO set of 1 794 terms) were selected for application validation. Precision, recall, and F1 score were calculated and compared horizontally with traditional dictionary tools, standalone large language models, and the similar application "RAG-HPO". Finally, replace the model with the more advanced ChatGPT-5 and evaluate its performance on the newly extracted dataset.
RESULTS:
An HPO term automatic annotation visualization application named PhenoRAG, based on large language models and RAG technology, was successfully developed. Users can access it directly via a web link. Across the 112 cases, a total of 2 150 HPO terms were generated; 2,064 (96.0%) were fully validated by the official database, with a hallucination rate of 1.3% and an HPO ID-name mismatch rate of 2.7%. After deduplication, 1,906 terms remained for testing. The overall precision was 63.65%, recall was 67.34%, and F1 was 65.44%, significantly outperforming traditional annotation tools (F1: 0.45-0.49, P < 0.001). Although PhenoRAG's F1 was lower than that of RAG-HPO (F1 = 0.78, P < 0.001), which relies on a manually constructed synonym database of 54 000 entries plus the HPO dataset, it requires no additional dictionary maintenance and can be used without any background in computer programming. Moreover, after switching to the GPT-5 model, PhenoRAG exhibited no hallucination rate on the new dataset, and its F1 score significantly increased (P = 0.038).
CONCLUSION
Without constructing a synonym database, the PhenoRAG achieved high-accuracy automatic mapping from clinical text to standard HPO terms. It features a low usage threshold, free access, and a Chinese-language interface, and can directly serve rare disease diagnosis, genetic counseling, and research scenarios in China and worldwide, warranting further clinical promotion and multicenter validation.
Humans
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Phenotype
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Biological Ontologies
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Language
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Software
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Large Language Models
2.Criteria for pancreas donor selection in islet transplantation and the experience of Changzheng hospital
Hanxiang ZHONG ; Junfeng DONG ; Wenyuan GUO ; Shengxian LI ; Hao YIN ; Yuanyu ZHAO ; Junsong JI
Organ Transplantation 2026;17(1):164-169
Diabetes mellitus, characterized by glucose metabolism disorders and marked by insulin deficiency or insulin resistance, has seen a continuous rise in prevalence. In recent years, islet transplantation has matured as a therapeutic approach for diabetes, becoming an important method for glycemic control and the reduction of diabetes-related complications. Donor selection directly influences transplant outcomes, and various research institutions worldwide have proposed multiple scoring systems to optimize donor assessment, such as the University of Alberta scoring system and the North American Islet Donor Score. This article explores the impact of key factors such as donor age, body mass index and ischemia time on islet transplantation. Combining practical experience in pancreatic donor selection from Shanghai Changzheng Hospital, it proposes screening criteria for pancreatic donors suitable for China, aiming to provide new evidence for improving the success rate of islet transplantation.
3.Bufalin reduces PD-L1 expression in colorectal cancer cells through suppressing TAM-mediated STAT3 phosphorylation
LU Chang1,2 ; SHANG Jing3 ; CHEN Jinbao4 ; ZHU Yuan2 ; ZHONG Jiani2 ; YIN Peihao1,5
Chinese Journal of Cancer Biotherapy 2026;33(4):373-378
[摘 要] 目的:探讨蟾毒灵(BU)对肿瘤相关巨噬细胞(TAM)介导的结直肠癌(CRC)细胞程序性死亡蛋白-配体1(PD-L1)表达的调控作用及其分子机制。方法:采用HCT116细胞与THP-1来源巨噬细胞构建体外共培养体系。佛波酯(PMA)诱导THP-1细胞分化为M0型巨噬细胞,进一步以HCT116细胞条件培养基(CM)刺激形成TAM样细胞。流式细胞术检测CD11b、CD206表达,以评价巨噬细胞极化水平;RT-qPCR及WB法检测TGF-β、IL-10、STAT3/p-STAT3及PD-L1表达变化;慢病毒转染构建STAT3敲低细胞系HCT116sh-STAT3,结合BU干预验证STAT3/PD-L1信号通路作用。结果:HCT116细胞CM可诱导巨噬细胞向M2表型极化,表现为CD11b⁺CD206⁺细胞比例升高(P < 0.01)及TGF-β、IL-10表达增加(均P < 0.001)。TAM条件培养基可显著促进HCT116细胞STAT3磷酸化(P < 0.001)并上调PD-L1 mRNA及蛋白表达水平(P < 0.001或P < 0.01)。BU干预后,TAM介导的STAT3磷酸化水平明显下降,PD-L1表达同步下调(均P < 0.01)。STAT3敲低可降低PD-L1表达,其作用趋势与BU一致。结论:BU可通过抑制TAM介导的STAT3信号激活,下调CRC细胞PD-L1表达,提示其在肿瘤免疫微环境调控中具有潜在的应用价值。
4.The expression and function of MST1 in prostate cancer
Yuhang HUANG ; Shiyuan YIN ; Linna FANG ; Kun ZHONG ; Guifang HE ; Yongping CAI ; Yu YIN
Acta Universitatis Medicinalis Anhui 2026;61(6):1045-1052
ObjectiveTo investigate the expression level of mammalian sterile 20-like kinase 1 (MST1) in prostate cancer (PCa) tissues, its biological functions, and its regulatory effects on androgen receptor (AR) and vascular endothelial growth factor (VEGF) expression. MethodsImmunohistochemistry was performed to detect MST1 expression in 77 prostate cancer tissues and 34 benign prostatic hyperplasia (BPH) tissues, and the relationship between MST1 expression and clinicopathological parameters was analyzed. MST1-overexpressing C4-2 and LNCaP cell lines were constructed. CCK-8 assay, Transwell migration assay, and angiogenesis assay were conducted to evaluate the effects of MST1 on cell proliferation, migration, and angiogenesis. The expression changes of AR and VEGF were detected by qRT-PCR and Western blot. ResultsMST1 expression was significantly lower in PCa tissues compared with BPH tissues (P=0.012). Low MST1 expression was significantly associated with tumor metastasis (P=0.033). MST1 overexpression inhibited C4-2 cell proliferation and migration, with transmembrane migrated cells reduced by 53.6% (P<0.01). MST1 overexpression decreased the mRNA and protein expression levels of AR and VEGF (P<0.05). Angiogenesis assay demonstrated that the length of new vessel structure was significantly reduced (P<0.05). ConclusionMST1 shows a low expression level in PCa tissues and is associated with tumor metastasis. MST1 exerts tumor-suppressive effects in prostate cancer by inhibiting cell proliferation, migration, and angiogenesis, as well as downregulating the expression of AR and VEGF, indicating its potential as a therapeutic target for prostate cancer.
5.Working practices in eliminating the public health crisis caused by viral hepatitis in Hainan Province of China
Weihua LI ; Changfu XIONG ; Taifan CHEN ; Bin HE ; Dapeng YIN ; Xuexia ZENG ; Feng LIN ; Biyu CHEN ; Xiaomei ZENG ; Biao WU ; Juan JIANG ; Lu ZHONG ; Yuhui ZHANG
Journal of Clinical Hepatology 2025;41(2):228-233
In 2022, Hainan provincial government launched the project for the prevention and control of viral hepatitis with the goals of a hepatitis B screening rate of 90%, a diagnostic rate of 90%, and a treatment rate of 80% among people aged 18 years and above by the year 2025, and the main intervention measures include population-based prevention, case screening, antiviral therapy, and health management. As of December 31, 2024, a total of 6.875 million individuals in the general population had been screened for hepatitis B, with a screening rate of 95.6%. A total of 184 710 individuals with positive HBsAg were identified, among whom 156 772 were diagnosed through serological reexamination, resulting in a diagnostic rate of 84.9%. A total of 50 742 patients with chronic hepatitis B were identified, among whom 42 921 had hepatitis B-specific health records established for health management, with a file establishment rate of 84.6%. A total of 31 553 individuals received antiviral therapy, with a treatment rate of 62.2%. A total of 2.503 million individuals at a high risk of hepatitis C were screened, among whom 4 870 tested positive for HCV antibody and 3 858 underwent HCV RNA testing, resulting in a diagnostic rate of 79.2%, and 1 824 individuals with positive HCV RNA were identified, among whom 1 194 received antiviral therapy, with a treatment rate of 65.5%. In addition, 159 301 individuals with negative HBsAg and anti-HBs and an age of 20 — 40 years were inoculated with hepatitis B vaccine free of charge. Through the implementation of the project for the prevention and control of viral hepatitis, a large number of hepatitis patients have been identified, treated, and managed in the province within a short period of time, which significantly accelerates the efforts to eliminate the crisis of viral hepatitis.
6.The path, dilemma, and countermeasures for patients to inform their families of the breaking bad news
Fengxing ZHONG ; Xiuping YIN ; Tiantian BAI
Chinese Medical Ethics 2025;38(1):116-122
Clinically, the occurrence of the breaking bad news is inevitable. For patients, they not only need to accept and cope with bad news, but also need to inform the bad news to their families with clear thinking and appropriate language, seeking their support and cooperation. This paper analysed the connotation and informing dilemma of bad news, investigated patients’ informing tendencies, as well as evaluated the advantages and disadvantages of three disclosure methods, including concealment, immediate informing, and staged informing. On these bases, a detailed response strategy for patients to inform their families was proposed in three parts, including pre-preparation, mid-articulation, and post-summary. In the initial phase, thorough preparation is essential. During the middle stage, when delivering bad news, use plain language and help family members adjust their emotions. In the final phase, ensure that all information and viewpoints have been fully communicated. In addition, the roles and analysis steps that doctors should play were analysed from their perspective and combined with the degree of doctor-patient trust. Effective informing of bad news is not only about communication skills, but also involves a deep understanding and respect for the psychological needs of patients and their families. Through meticulous preparation, appropriate expression, emotional support, and clear confirmation, communication and trust are promoted to face and overcome difficulties together.
7.Prognostic Factors of Liposarcoma in Head and Neck
Shuo DING ; Zhigang HUANG ; Jugao FANG ; Yang ZHANG ; Lizhen HOU ; Wei GUO ; Gaofei YIN ; Qi ZHONG
Cancer Research on Prevention and Treatment 2025;52(1):31-35
Objective To explore the pathogenesis and prognostic factors of liposarcoma in the head and neck region, and simultaneously analyze the efficacy of different treatment regimens. Methods A retrospective analysis was performed on all patients with primary untreated head and neck liposarcoma who were diagnosed and underwent surgical treatment at our hospital from January 2008 to January 2024. All patients were monitored during follow-up, and their prognoses were analyzed using SPSS software. Results A total of 30 patients were included in the study. Liposarcoma accounted for up to 60% of the cases in the orbit, while the remaining liposarcomas were primarily located in various interspaces of the neck. Dedifferentiated liposarcoma was the most common type, comprising 33%, while myxoid pleomorphic liposarcoma was the rarest at 4%. The tumor pathological type (P<0.001) and Ki67 (P=0.014) significantly affected the tumor control rate. However, an analysis of disease-specific survival rates revealed no significant differences across various factors (all P>0.05). Conclusion The prognosis of head and neck liposarcoma is better compared to that of liposarcomas in other parts of the body. However, myxoid pleomorphic liposarcoma, pleomorphic fat sarcoma, and high Ki67 levels are indicators of poor prognosis. Additionally, postoperative adjuvant radiotherapy does not significantly enhance disease-specific survival rates.
9.Textual Research on the Origin and Evolution of Olfactory Diagnosis in Traditional Chinese Medicine
Zijian XU ; Qian FU ; Yin JIANG ; Xiaoyu ZHANG ; Rui ZHONG ; Zhouyou WU ; Hongcai SHANG ; Mei ZHANG
World Science and Technology-Modernization of Traditional Chinese Medicine 2025;27(10):2790-2799
Olfactory diagnosis refers to the method of diagnosing diseases by smelling the odor emitted from the patient's body,secretions and excreta,and the odor of the sick room.It is one of the important diagnostic methods under the guidance of traditional Chinese medicine(TCM)theory,and is included in the"inquiry and olfaction"of TCM.In recent years,there has been rapid development in medical-engineering integration,artificial intelligence,big data,and other interdisciplinary fields.This has been promoting the TCM gradually to develop towards accurate,efficient and personalized medical treatment,which has opened a new era of"Smart TCM".In this paper,the ancient literature related to olfactory diagnosis was systematically reviewed,the developmental characteristics of olfactory diagnosis theories in various periods was sorted out,and the different views of TCM specialists on the odors emitted by the human body in physiological and pathological states was summarized.The paper is to explore the origin of TCM olfactory diagnosis and its periodization,clarify the diagnosis of abnormal odors,corresponding to the nature,etiology and prognosis of the disease,and clarify the development of TCM olfactory diagnosis.It provides a theoretical source and literature basis for promoting the research of"smart olfactory diagnosis of TCM"and facilitating the development of objectivity,standardization and intelligence of olfactory diagnosis in TCM.
10.Diagnosis and Treatment of a Case of Spironolactone-Associated Asymptomatic Hyperuricemia After Renal Transplantation
Yun XIAO ; Xiaoyu HAN ; Chao ZHENG ; Yu FU ; Hanbin XIONG ; Bin ZOU ; Baolin WANG ; Hua ZOU ; Chenglong YIN ; Zhengyao JIANG ; Sheng ZOU ; Anle DU ; Guohui LI ; Xiaohui GUO ; Lin ZHONG ; Jiake HE
Herald of Medicine 2025;44(10):1562-1565
Objective To explore the identification method,pathogenesis,clinical characteristics and individualized pharmacotherapy of asymptomatic hyperuricemia after renal transplantation.Methods The pharmacist was on duty at the organ transplant outpatient clinic.During this time,they analyzed and sorted out the medications,identified and differentiated a case of asymptomatic hyperuricemia related to spironolactone in a patient who had undergone a renal transplant,and provided comprehensive care throughout the entire process.Results The asymptomatic hyperuricemia in this patient might be associated with spironolactone,and the adverse reactions of the patient were alleviated by pharmacists through optimizing clinical treatment.Up to now,no hyperuricemia occurred.Conclusions Pharmacists are required to collaborate closely with clinicians to establish medication profiles for patients under long-term follow-up and to closely monitor and evaluate drug-related adverse reactions.Additionally,they should assess the renal function and immune status of transplant recipients promptly and formulate individualized treatment plans in order to enhance the long-term survival of both the transplanted kidneys and the recipients.

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